Plenty of boys are named after their fathers. I think it is better if there are different nicknames. So John and Jack , Bill and Will, Ted and Ed etc.
I have 2 cousins with the same name but again it is a name with a host of nicknames (though they both chose the same one in the end) and they are not that close in age. I think it depends on how much you would see your nephew and if they would be called exactly the same name (not different nicknames).
My only real concern is that people seem to place much more importance on having a name that no others in the class/family etc have nowadays. Until relatively recently parents by and large chose from a much smaller pool of names, often using the same names in each generation. This meant that knowing lots of people with the same name as you was far more accepted than I think it is now.